S.T.
I am so sorry! All the things I would have suggested were the cause of the problem (Soda, fluoride, ect) aren't!! You are right to be concerned about the fluoride. Excessive fluoride causes fluoridosies which would weaken not strengthen the teeth. http://www.fluoridealert.org/dental-fluorosis.htm
Do look into the effects of fluoride on the body (www.mercola.com has some) and find a different dentist- maybe an oral surgeon. I really liked Dr Hoffman in Clear Lake but I don't know if he does babies.
There IS fluoride in the water but probably not enough to cause a problem with his teeth, unless he's especially sensitive to it.